On Christmas Eve 1950, Hamilton, along with three other student Scottish nationalists, removed the Stone of Scone from its place under the Coronation Chair in Westminster Abbey, London. The Stone, originally used for the coronation of Scottish monarchs, had been removed to England by Edward I in 1296 to bolster his claim to the throne of Scotland. After the Acts of Union 1707 between Scotland and England, it was used for the coronation of British monarchs. As such, Hamilton's action in returning the Stone to Scotland was applauded as a symbolic triumph for Scottish nationalism. The Stone was turned over to the Church of Scotland, which surrendered it to English authorities in April 1951. Hamilton and his accomplices were charged, but never prosecuted. The Stone was eventually returned to Scotland in 1996, with provision for subsequent use in the coronation of British monarchs.

When first admitted to the bar as a young advocate in 1953, Hamilton refused to swear allegiance to Queen Elizabeth II arguing that she could only be referred to as "Queen Elizabeth" (sans regnal number) in Scotland as the regnal numbers counted Queen Elizabeth I, who had not ruled over Scotland or any of the subsequent united kingdoms which it has entered into. MacCormick v. Lord Advocate, which Hamilton brought with rector John MacCormick against the Crown, failed. The Inner House of the Scottish Court of Session held that the monarch's title is the sole prerogative of the sovereign, and the Crown had accepted a system whereby regnal numbers were taken from the larger of both former kingdoms in the United Kingdom, that is England and not Scotland. (It was later suggested by Winston Churchill after the accession of Elizabeth II that, in the future, the higher of the two numerals from the English and Scottish sequences would be used. This system has yet to be put to the test).

Hamilton has written two autobiographical works, that are also in part polemical, A Touch of Treason (1990) and A Touch More Treason (1994). He has launched a blog, where he posts commentary on Scottish social and political life.

In February 2009, BBC News and The Daily Telegraph reported that Hamilton was suing the Royal Bank of Scotland (RBS) over claims they had mis-sold shares to him in April 2008.[3] Hamilton purchased 640 shares at £2 per share as part of a £12 billion rights issue. The writ he lodged in court claimed that the bank invited shareholders, including him and his wife, to invest in a rights issue, an offer that he took up on her behalf. The writ further alleged that RBS induced him to invest his money by "concealing the true state of their finances".[4] He further alleged that the bank was "negligent in representing themselves as solvent at all material times when in fact they were insolvent".[3]

RBS stated they would defend themselves vigorously against the claims made by Hamilton,[3] but he dropped the case on 26 February 2009 after the small claims court refused to deal with it, citing the legal and factual complexity of the case, which would require trial in a higher court.[5]

In 2008, Hamilton's book, The Taking of the Stone of Destiny, was made into a movie entitled Stone of Destiny. The film depicted Hamilton as the protagonist leading a team of students to reclaim the Stone of Scone. Additionally, Hamilton had a small, cameo role.[6]